Hi Michele,
I think that’s the problem then. The freesurfer code is written to work with
the specific version of minc that we distribute with the release. If possible,
you should run freesurfer without setting any MINC paths to your local install
to see if that fixes things.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti
<michele.valo...@gmail.com>
Date: Thursday, February 11, 2021 at 11:02 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mincRead error
External Email - Use Caution
Hi Trisanna,
thank you for your reply, I am using minc2 (version 1.9.16) but this is the
same version I use on my local machine and it does not give any errors there,
and SetUpFreesurfer is sourced before exporting MINC paths and variables.
Michele
On Wed, 10 Feb 2021 at 14:57, Trisanna Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>>
wrote:
External Email - Use Caution
Hi All
As a frequent user of minctools, I know I’ve had problems in the past if I
source minctools before sourcing freesurfer in the same terminal, because
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.
Best,
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hoopes, Andrew"
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error
Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed
minc tools separately on your local machine and do you have any of these
variables set in your default environment?
MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR
It’s possible there’s another install of MNI that’s interfering with the
freesurfer one.
Andrew
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Michele Valotti
<michele.valo...@gmail.com<mailto:michele.valo...@gmail.com>>
Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mincRead error
External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version
on my local machine (where the command runs) and in the cloud instance
On Fri, 5 Feb 2021 at 18:02, Michele Valotti
<michele.valo...@gmail.com<mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local
machine I tried to run it on a server (which should however have the same
FreeSurfer version and setup), but I am getting this error
mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34
UTC 2020 x86_64 GNU/Linux
recon-all -s base_freesurfer exited with ERRORS at Fri Feb 5 17:45:34 UTC 2021
Any idea what the cause of this might be?
Thank you!
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